Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P
Query= TCDB::P0AAG3 (241 letters) >FitnessBrowser__Phaeo:GFF1143 Length = 259 Score = 206 bits (523), Expect = 5e-58 Identities = 108/251 (43%), Positives = 159/251 (63%), Gaps = 10/251 (3%) Query: 1 MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60 ++ ++ + K YG +V+ +G+VV + G SGSGKSTL++ N LE Q+G+I Sbjct: 7 VLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQEGDILF 66 Query: 61 DGIVVNDKKTDLAK----------LRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDK 110 G +N T LA+ +R+ + MVFQ F L+ H++I++N+ A + VL RD+ Sbjct: 67 KGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLTVLGRDR 126 Query: 111 APAREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPE 170 A + A K L +VG+ + +PAQLSGGQQQR AIARALCM+P A+LFDEPTSALDPE Sbjct: 127 AEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPTSALDPE 186 Query: 171 MINEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSD 230 + EV+ V+ +LA EG TM++VTH+M A V++ ++F+ +G I E+ D F +S+ Sbjct: 187 LEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVFGSTRSE 246 Query: 231 RAKDFLAKILH 241 R + FLA H Sbjct: 247 RLRGFLASTRH 257 Lambda K H 0.320 0.135 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 156 Number of extensions: 4 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 241 Length of database: 259 Length adjustment: 24 Effective length of query: 217 Effective length of database: 235 Effective search space: 50995 Effective search space used: 50995 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory